Data open sharing becomes the basis for mining the potential value of big data. Due to the different structure of different shared data sources, the upper layer application is restricted. Therefore, how to establish a unified and user friendly logical organization form is an urgent problem to be solved in the open sharing of data. This paper presents a method of data organization based on ontology knowledge base. Firstly, we design rules to extract the concepts and relationships in the original data set. Then we implement three standardized human-computer interaction interfaces to perfect the ontology model. Finally, according to the ontology knowledge base model, original data set is reorganized, which makes the logic structure of the new data set more suitable to the upper level application, and improves the utilization ratio of the open data.